Article
Biotechnology & Applied Microbiology
Kalimullah Saighani, Daiki Kondo, Naoto Sano, Kazumasa Murata, Tetsuya Yamada, Motoki Kanekatsu
Summary: The integrity of embryonic RNAs required for germination in rice seeds is positively correlated with seed longevity. RIN values can serve as a quantitative indicator to evaluate germinability in rice.
PLANT BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Pernille Sos Hovgaard Jensen, Maja Johansen, Lasse K. Bak, Lars Juhl Jensen, Christina Kjaer
Summary: Study finds that gene expression analysis may be influenced by pre-analytical factors, but the collection time, tissue size, collection method, and RNA isolation method do not significantly affect the yield and integrity of brain-derived RNA, with potential practical and financial implications for clinical genomic departments and other laboratory settings.
NEUROCHEMICAL RESEARCH
(2021)
Article
Chemistry, Medicinal
Irena Voinsky, Elad Shapira, David Gurwitz
Summary: Biobanks play a crucial role in biomedical research by providing human cell lines for drug development projects. RNA-sequencing of large panels of cell lines from individuals with certain disorders and healthy controls, or with different drug response phenotypes, is commonly performed. In this study, we demonstrate that extracting RNAs directly from long-term frozen human cell lines yields high-quality RNA samples suitable for optimal RNA-sequencing, comparable to those obtained from growing cell lines.
DRUG DEVELOPMENT RESEARCH
(2023)
Article
Cell Biology
Saije K. Morosin, Sarah J. Delforce, Celine Corbisier de Meaultsart, Eugenie R. Lumbers, Kirsty G. Pringle
Summary: The study suggests that FURIN may not be crucial for syncytialisation in human trophoblast cells, and there may be other proteases involved, especially in primary trophoblasts. The findings contradict previous research, indicating potential differences in the role of FURIN in syncytialisation among trophoblast cells from different gestational periods.
CELL DEATH & DISEASE
(2021)
Article
Psychiatry
Kazusa Miyahara, Mizuki Hino, Zhiqian Yu, Chiaki Ono, Atsuko Nagaoka, Masataka Hatano, Risa Shishido, Hirooki Yabe, Hiroaki Tomita, Yasuto Kunii
Summary: This study evaluated the effects of pH and RIN on gene expression in human postmortem brain tissue. It found that 24.7% of genes were influenced by pH, 36.3% were influenced by RIN, and 15.6% were influenced by both factors. These genes were associated with energy production, the immune system, the cell cycle, and RNA processing. These findings are important for controlling confounders in future postmortem brain studies.
FRONTIERS IN PSYCHIATRY
(2023)
Article
Multidisciplinary Sciences
Ashley N. Hall, Tychele N. Turner, Christine Queitsch
Summary: The study investigated copy number variation of ribosomal RNA genes (rDNA) and found no differences in probands with autism spectrum disorder and unaffected siblings. Validation results suggest that the previously reported concerted copy number variation between 45S and 5S arrays may be due to variable data quality, and meaningful correlation between 45S and 5S copy numbers was not detected in various datasets.
SCIENTIFIC REPORTS
(2021)
Article
Developmental Biology
Kendra Naismith, Brian Cox
Summary: This study generated 235 human placenta and trophoblast specific gene sets through re-analysis of 330 microarray and 91 RNA sequencing experiments. These new placental gene sets revealed unique subnetworks compared to Gene Ontology. When applied to investigations on preeclampsia, fetal growth restriction, invasive tumors, and cell models, the gene sets showed matching terms related to cell types and oxygen tension.
Article
Immunology
Alexa A. Freedman, Britney P. Smart, Lauren S. Keenan-Devlin, Janedelie Romero, Andrew Franklin, Ann Borders, Linda M. Ernst, Gregory E. Miller
Summary: The study aimed to investigate temporal changes in placental gene expression by longitudinally sampling placentas over a 24-hour period. Results indicated that for some mRNA transcripts, expression changes as time to sample collection increases.
AMERICAN JOURNAL OF REPRODUCTIVE IMMUNOLOGY
(2021)
Article
Biochemical Research Methods
Yi Wang, Stephanie C. Hicks, Kasper D. Hansen
Summary: Estimates of correlation between genes in co-expression analysis are commonly used to construct gene networks. However, the distribution of these correlations depends on the observed expression level, resulting in a higher correlation for highly expressed genes. This relationship is not observed in protein-protein interaction data, indicating that it is not biologically relevant. To address this issue, we propose a method called spatial quantile normalization (SpQN) that normalizes local distributions in a correlation matrix, removing the mean-correlation relationship and correcting expression bias in network reconstruction.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Clinical Neurology
Mehrdad A. Estiar, Konstantin Senkevich, Eric Yu, Parizad Varghaei, Lynne Krohn, Sara Bandres-Ciga, Alastair J. Noyce, Guy A. Rouleau, Ziv Gan-Or
Summary: There is no evidence for a causal relationship or genetic correlation between restless legs syndrome and Parkinson's disease. The associations observed in epidemiological studies could be attributed, in part, to confounding or nongenetic determinants.
MOVEMENT DISORDERS
(2021)
Article
Multidisciplinary Sciences
Tobias J. Kraemer, Per Huebener, Bruno Poettker, Christina Goelz, Axel Neulen, Tobias Pantel, Hermann Goetz, Katharina Ritter, Michael K. E. Schaefer, Serge C. Thal
Summary: This study suggests that early treatment with RNase1 after traumatic brain injury can reduce secondary damage, stabilize the blood-brain barrier, and suppress neuroinflammation, but it does not have a significant impact on lesion volume and function.
SCIENTIFIC REPORTS
(2022)
Article
Medicine, General & Internal
Jaroslav Pelisek, Yankey Yundung, Benedikt Reutersberg, Lorenz Meuli, Fabian Rossler, Laetitia Rabin, Reinhard Kopp, Alexander Zimmermann
Summary: Proper biobanking is crucial for reliable data in next-generation sequencing. Diseased vascular tissues with low RNA quality pose a challenge. The study investigated RNA isolation methods, admission solutions, RIN determination, and gene expression analysis from vascular samples in the Swiss Vascular Biobank (SVB).
JOURNAL OF CLINICAL MEDICINE
(2023)
Article
Biochemical Research Methods
Qunlun Shen, Shihua Zhang
Summary: With the rapid accumulation of biological omics datasets, finding the relationships of genes across datasets has become a crucial issue. The proposed Approximate Distance Correlation (ADC) method efficiently selects interrelated genes across two different biological datasets and demonstrates effectiveness with simulation data and real applications. The number of highly interrelated genes identified by ADC can serve as a metric to measure the similarity between datasets, characterizing the relative differences in cell types and technologies.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Cell Biology
Catia Andreassi, Raphaelle Luisier, Hamish Crerar, Marousa Darsinou, Sasja Blokzijl-Franke, Tchern Lenn, Nicholas M. Luscombe, Giovanni Cuda, Marco Gaspari, Adolfo Saiardi, Antonella Riccio
Summary: The 3' untranslated regions (3' UTRs) of mRNA play essential roles in mRNA metabolism, with incorrect processing potentially leading to developmental defects and neurological disorders. Deep sequencing revealed cleavage of 3' UTRs in transcripts in sympathetic neuron axons, generating translatable isoforms crucial for axon integrity. This study provides insights into mRNA metabolism that regulates local protein synthesis and generates a new class of 3' UTR-derived RNAs.
Article
Immunology
Jiayao Ou, Xiaoxing Guan, Jiali Wang, Tianjiao Wang, Bin Zhang, Rong Li, Huji Xu, Xiaoyu Hu, Xue-Kun Guo
Summary: The NELF complex plays a critical role in maintaining epithelial homeostasis in intestinal epithelial cells by sustaining expression of genes related to junctional integrity. Lack of NELF results in impaired barrier integrity and exacerbated inflammation in the intestine, highlighting the importance of elongation in defining the IEC transcriptome.
MUCOSAL IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Julia F. Litzky, Maya A. Deyssenroth, Todd M. Everson, David A. Armstrong, Luca Lambertini, Jia Chen, Carmen J. Marsit
Article
Biochemistry & Molecular Biology
Shouneng Peng, Maya A. Deyssenroth, Antonio F. Di Narzo, Luca Lambertini, Carmen J. Marsit, Jia Chen, Ke Hao
HUMAN MOLECULAR GENETICS
(2017)
Article
Multidisciplinary Sciences
Huan Wang, Aaron Bender, Peng Wang, Esra Karakose, William B. Inabnet, Steven K. Libutti, Andrew Arnold, Luca Lambertini, Micheal Stang, Herbert Chen, Yumi Kasai, Milind Mahajan, Yayoi Kinoshita, Gustavo Fernandez-Ranvier, Thomas C. Becker, Karen K. Takane, Laura A. Walker, Shira Saul, Rong Chen, Donald K. Scott, Jorge Ferrer, Yevgeniy Antipin, Michael Donovan, Andrew V. Uzilov, Boris Reva, Eric E. Schadt, Bojan Losic, Carmen Argmann, Andrew F. Stewart
NATURE COMMUNICATIONS
(2017)
Article
Environmental Sciences
Todd M. Everson, Tracy Punshon, Brian P. Jackson, Ke Hao, Luca Lambertini, Jia Chen, Margaret R. Karagas, Carmen J. Marsit
ENVIRONMENTAL HEALTH PERSPECTIVES
(2018)
Article
Endocrinology & Metabolism
W. Zhang, Q. Li, M. Deyssenroth, L. Lambertini, J. Finik, J. Ham, Y. Huang, K. J. Tsuchiya, P. Pehme, J. Buthmann, S. Yoshida, J. Chen, Y. Nomura
JOURNAL OF NEUROENDOCRINOLOGY
(2018)
Article
Pediatrics
Julia F. Litzky, Maya A. Deyssenroth, Todd M. Everson, Barry M. Lester, Luca Lambertini, Jia Chen, Carmen J. Marsit
PEDIATRIC RESEARCH
(2018)
Article
Environmental Sciences
Maya A. Deyssenroth, Chris Gennings, Shelley H. Liu, Shouneng Peng, Ke Hao, Luca Lambertini, Brian P. Jackson, Margaret R. Karagas, Carmen J. Marsit, Jia Chen
ENVIRONMENT INTERNATIONAL
(2018)
Article
Obstetrics & Gynecology
Richard Jones, Juan Pena, Elana Mystal, Carmen Marsit, Men-Jean Lee, Joanne Stone, Luca Lambertini
JOURNAL OF MATERNAL-FETAL & NEONATAL MEDICINE
(2020)
Article
Genetics & Heredity
Shouneng Peng, Maya A. Deyssenroth, Antonio F. Di Narzo, Haoxiang Cheng, Zhongyang Zhang, Luca Lambertini, Arno Rusualepp, Jason C. Kovacic, Johan L. M. Bjorkegren, Carmen J. Marsit, Jia Chen, Ke Hao
Article
Environmental Sciences
Todd M. Everson, Carmen Marable, Maya A. Deyssenroth, Tracy Punshon, Brian P. Jackson, Luca Lambertini, Margaret R. Karagas, Jia Chen, Carmen J. Marsit
ENVIRONMENTAL HEALTH PERSPECTIVES
(2019)
Article
Public, Environmental & Occupational Health
L. Lambertini, Q. Li, Y. Ma, W. Zhang, K. Hao, C. Marsit, J. Chen, Y. Nomura
JOURNAL OF DEVELOPMENTAL ORIGINS OF HEALTH AND DISEASE
(2019)
Article
Endocrinology & Metabolism
Carolina Rosselot, Anil Kumar, Jayalakshmi Lakshmipathi, Pili Zhang, Geming Lu, Liora S. Katz, Edward Prochownik, Andrew F. Stewart, Luca Lambertini, Donald K. Scott, Adolfo Garcia-Ocana
Article
Biochemistry & Molecular Biology
Maya A. Deyssenroth, Carmen J. Marsit, Jia Chen, Luca Lambertini
Article
Biochemistry & Molecular Biology
Elizabeth Kennedy, Todd M. Everson, Tracy Punshon, Brian P. Jackson, Ke Hao, Luca Lambertini, Jia Chen, Margaret R. Karagas, Carmen J. Marsit
Review
Biochemistry & Molecular Biology
Carolina Rosselot, Sharon Baumel-Alterzon, Yansui Li, Gabriel Brill, Luca Lambertini, Liora S. Katz, Geming Lu, Adolfo Garcia-Ocana, Donald K. Scott
Summary: Recent studies suggest that appropriate levels of Myc could have therapeutic potential for beta-cell regeneration by enhancing cell replication without inducing cell death or loss of insulin secretion. Previous studies using pathophysiological or supraphysiological levels of Myc reported enhanced beta-cell death, dedifferentiation, or formation of insulinomas, reducing enthusiasm for Myc as a therapeutic target.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
